[BioRuby] selenoproteins

[GOTO Naohisa]

Hi,

On Tue, 15 Jun 2004 18:11:48 +0200
Michael Han <m.han at gsf.de> wrote:

> Hi everyone,
> 
> i am working on fine-tuning an annotation pipeline with ruby.
> As selenoproteins seem not to be supported by BioRuby, they break my 
> assertions (and most gene predictions).
> Therefore i would like to add a codon-table for selenoproteins (TGA=>U).

In next version, Bio::Sequence::NA#translate and Bio::CodonTable will be
changed, and users will be able to modify codon tables freely based on
NCBI taxonomy's definitions or from scratch. We'll soon commit new codes
into CVS in few days.

> Also i would like to ask if there are people working on support for 
> BLAT / BED / PSL / moving tests into separate Test::Unit classes.

I have some codes to support BLAT (psl and pslx format)
but not refined and not added to bioruby yet. (In addition,
I have some primitive codes to support sim4, est2genome and spidey.)

I'm sorry I don't know much about BED ('Brain Est Database' ?).
Unit tests are important but, in bioruby, only few efforts
have been done yet.

Regards,
-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Genome Information Research Center, Osaka University, Japan